TY - JOUR U1 - Zeitschriftenartikel, wissenschaftlich - begutachtet (reviewed) A1 - Bernardi, Austen A1 - Faller, Roland A1 - Reith, Dirk A1 - Kirschner, Karl N. T1 - ACPYPE update for nonuniform 1–4 scale factors: Conversion of the GLYCAM06 force field from AMBER to GROMACS JF - SoftwareX N2 - Herein we report an update to ACPYPE, a Python3 tool that now properly converts AMBER to GROMACS topologies for force fields that utilize nondefault and nonuniform 1–4 electrostatic and nonbonded scaling factors or negative dihedral force constants. Prior to this work, ACPYPE only converted AMBER topologies that used uniform, default 1–4 scaling factors and positive dihedral force constants. We demonstrate that the updated ACPYPE accurately transfers the GLYCAM06 force field from AMBER to GROMACS topology files, which employs non-uniform 1–4 scaling factors as well as negative dihedral force constants. Validation was performed using β-d-GlcNAc through gas-phase analysis of dihedral energy curves and probability density functions. The updated ACPYPE retains all of its original functionality, but now allows the simulation of complex glycomolecular systems in GROMACS using AMBER-originated force fields. ACPYPE is available for download at https://github.com/alanwilter/acpype. KW - ACPYPE KW - Nonbonded scaling factor KW - Force field KW - Carbohydrate KW - Gromacs KW - Glycam06 SN - 2352-7110 SS - 2352-7110 U6 - https://doi.org/10.1016/j.softx.2019.100241 DO - https://doi.org/10.1016/j.softx.2019.100241 VL - 10 PB - Elsevier ER -